Obtaining genotype information on thousands of polymorphisms in a highly parallel fashion is becoming an increasingly important task in mapping disease loci, in identifying quantitative trait loci, in diagnosing tumor loss of heterozygosity, and in performing association studies. A currently available method for simultaneously evaluating large numbers of genetic polymorphisms involves hybridization to allele-specific probes on high density oligonucleotide arrays. In order to practice that method, redundant sets of hybridization probes, typically twenty or more, are used to score each allelic marker. A high degree of redundancy is required to reduce noise and achieve an acceptable level of accuracy. Even this level of redundancy is insufficient to unambiguously score heterozygotes or to quantitatively determine allele frequency in a population.
The technique of allele-specific polymerase chain reaction (ASPCR) can be applied to allele identification and quantitative analysis of allele frequency. However, this technique suffers from cross reactivity between amplified products when hybridizing to probes which differ by only a single nucleotide base. A partial solution to the cross-reactivity problem has been achieved by the addition of sequence tags to the ASPCR primers. The incorporation of tags in ASPCR primers can itself interfere with the identification of the amplification products because unreacted primers or partially extended products can compete with full products for hybridization to the probes. Thus, there is a further need in the art for methods and materials which permit the accurate determination of polymorphic loci without interference from incompletely reacted products.